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bilayer-membrane
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The role of mscl amphipathic n terminus indicates a blueprint for bilayer-mediated gating of mechanosensitive channels
, Article Nature Communications ; Volume 7 , 2016 ; 20411723 (ISSN) ; Cortes, D. M ; Cox, C. D ; Rohde, P. R ; Liu, W ; Deitmer, J. W ; Bavi, O ; Strop, P ; Hill, A. P ; Rees, D ; Corry, B ; Perozo, E ; Martinac, B ; Sharif University of Technology
Nature Publishing Group
2016
Abstract
The bacterial mechanosensitive channel MscL gates in response to membrane tension as a result of mechanical force transmitted directly to the channel from the lipid bilayer. MscL represents an excellent model system to study the basic biophysical principles of mechanosensory transduction. However, understanding of the essential structural components that transduce bilayer tension into channel gating remains incomplete. Here using multiple experimental and computational approaches, we demonstrate that the amphipathic N-terminal helix of MscL acts as a crucial structural element during tension-induced gating, both stabilizing the closed state and coupling the channel to the membrane. We...
Dynamics of Protein-Embedded Vesicles in Simple Shear Flow
, M.Sc. Thesis Sharif University of Technology ; Jalali, Mir Abbas (Supervisor) ; Khoshnood, Atefeh (Co-Advisor)
Abstract
Studying the dynamics of vesicles in simple shear flow is the first step to decipher the dynamics of cells in flows or the motion of vesicle-based nanoparticles in vessels for drug delivery. The deformation of vesicle in shear flow changes the permeability of its membrane and may lead to its rupture, both of which correlate with the transportation of vesicle cargos to their environment, especially important in drug delivery. The deformation of vesicles in shear flow not only depends on the physical properties of the whole system, such as temperature, but also on the mechanical properties of three media: vesicle membrane plus vesicle’s inner and outer fluid. The effect of the mechanical...
Kinetics of Animal Cell Adhesion Mediated by the Diffusion of Cell Wall Receptors: Effect of Mechanical Stiffness and Electrical Charges of the Substrate
, M.Sc. Thesis Sharif University of Technology ; Mohammadi Shoja, Hossein (Supervisor)
Abstract
Viability and proliferation of cells in cell culture mainly depends on i) cell culture medium, ii) cell-cell interaction, and iii) the supporting scaffold. Among these factors, and within recent years, surface and mechanical properties of the supporting ECM has attracted many researchers. Experiment results show that the animal cell adhesion is accelerated on stiffer scaffolds. Electrical charge of the scaffold is also a determinant term in the kinetics of adhesion and on a relatively charged scaffold, one can expect an increment in kinetics of adhesion front movement. This is due to the natural negative charges of the cell wall membrane. In this thesis, an analytical model is proposed to...
Protein Aggregation in Biological Membrane
, M.Sc. Thesis Sharif University of Technology ; Jalali, Mir Abbas (Supervisor) ; Ejtehadi, Mohammad Reza (Co-Advisor)
Abstract
Aggregation of membrane proteins plays a determinative role in many biological processes، such as signal transduction, cell division and endocytosis. In the present study, we have investigated the interaction between proteins in vesicles by means of coarse-grained molecular dynamics simulations. In the first step, a number of periodic lipid bilayers were simulated and their physical properties were calculated. Then, bilayers were immersed in water and converted into spherical vesicles via a selforganizing process . Finally two proteins were embedded into the vesicle and the potential of mean force (PMF) respect to the angle between them was obtained using umbrella sampling. This process was...
Fluorescent quantification of size and lamellarity of membrane nanotubes
, Article European Biophysics Journal ; Vol. 43, Issue. 12 , 2014 , pp. 595-602 ; ISSN: 1432-1017 ; Oddershede, L. B ; Reihani, S. N. S ; Bendix, P. M ; Sharif University of Technology
Abstract
Membrane nanotubes, ubiquitous in cellular systems, adopt a spectrum of curvatures and shapes that are dictated by their intrinsic physical characteristics as well as their interactions with the local cellular environment. A high bending flexibility is needed in the crowded cytoplasm where tubes often need to bend significantly in the axial direction at sub-micron length scales. We find the stiffness of spontaneously formed membrane nanotubes by measuring the persistence length of reconstituted membrane nanotubes freely suspended in solution and imaged by fluorescence microscopy. By quantifying the tube diameter we demonstrate for the first time that the persistence length scales linearly...
Modeling self-assembly of the surfactants into biological bilayer membranes with special chemical structures using dissipative particle dynamics method
, Article Scientia Iranica ; Volume 23, Issue 3 , 2016 , Pages 942-950 ; 10263098 (ISSN) ; Pishevar, A. R ; Saidi, M. S ; Shirani, E ; Sharif University of Technology
Sharif University of Technology
2016
Abstract
The aim of this study is to simulate the self-assembly of the surfactant molecules with special chemical structure and bending stiffiness into bilayer membranes using a mesoscopic Dissipative Particle Dynamics (DPD) method. The surfactants are modeled with special chemical structure and bending stiffiness. To confirm that the novel model is physical, we determine the interaction parameters based on matching the compressibility and solubility of the DPD system with real physics of the uid. To match the mutual solubility for binary uids, we use the relation between DPD parameters and x-parameters in Flory-Huggins-type models. Unsaturated bonds can change the stiffiness of a lipid membrane,...
Lipid membranes with transmembrane proteins in shear flow
, Article Journal of Chemical Physics ; Volume 132, Issue 2 , 2010 ; 00219606 (ISSN) ; Noguchi, H ; Gompper, G ; Sharif University of Technology
Abstract
The effects of embedded proteins on the dynamical properties of lipid bilayer membranes are studied in shear flow. Coarse-grained molecular simulations are employed, in which lipids are modeled as short polymers consisting of hydrophilic head groups and hydrophobic tail monomers; similarly, transmembrane proteins are modeled as connected hydrophobic double- or triple-chain molecules with hydrophilic groups at both ends. In thermal equilibrium, rigid proteinlike molecules aggregate in a membrane of flexible lipids, while flexible proteins do not aggregate. In shear flow parallel to the membrane, the monolayers of lipid bilayer slide over each other. The presence of transmembrane proteins...
Electromagnetic performance, optical and physiochemical features of CaTiO3/NiO and SrFe12O19/NiO nanocomposites based bilayer absorber
, Article Journal of Colloid and Interface Science ; Volume 610 , 2022 , Pages 879-892 ; 00219797 (ISSN) ; Liu, J ; Huynen, I ; Mahmoud, M. Z ; Akhtar, M. N ; Sharif University of Technology
Academic Press Inc
2022
Abstract
Herein, two distinct nanocomposites of CaTiO3 micro-cubes and polygonal SrFe12O19, both decorated with NiO nanoparticles, were successfully synthesized using hydrothermal method. The physico-chemical features of as-prepared samples were evaluated via XRD, FTIR, UV–vis, BET, XPS, FESEM and EDS analysis. Microwave attenuation features of as-prepared single layer absorbers were determined by VNA analysis in 2–18 GHz. Simulation confirmation was checked by preparing a bi-layer samples and evaluating it using VNA analysis after finding the appropriate thickness of each layer. The reflection loss from each single layer samples containing 20 wt% of each CaTiO3/NiO and SrFe12O19/NiO nanocomposites...